Francis James Gillen was born of Irish parents who emigrated to Australia in 1855, and originally settled in the Cavan, South Australia, area. It was not long before they moved to Clare, South Australia, where Francis spent his early years.

On 15 January 1867, aged eleven, Francis joined the Public Service as a telegraph messenger. At fifteen, he was transferred to Adelaide as a junior assistant, and it was from this time that he studied at the School of Mines in the evenings. With the construction of the Overland Telegraph Line (O. T. L.) in the 1870s, Gillen was rapidly promoted and in 1875 was posted to Alice Springs as an operator with the O. T. L In December 1892 he was made Post and Telegraph Master in charge of an extensive area.

Gillen's time spent in the Northern Territory meant that he often came into contact with the local Aboriginal people, for whom he developed an abiding interest, and deep affection and regard. He learned the Aranda's language and was admitted as a fully initiated member of their tribe. He was known by them as 'Oknirrabata', which means 'great teacher', an honour that enabled him to attend ceremonies and be given information about tribal law and rituals.

In 1894, Gillen met Baldwin Spencer who visited Alice Springs with the Horn Expedition. Spencer encouraged Gillen to pursue his anthropological interest, and promised to collaborate with him in publishing a book. This inspired Gillen to collect and record as much information as he could on the Aboriginal people of the area. Gillen had refused two major inducements to leave the centre, preferring to stay and continue his anthropological work after being encouraged by Spencer. Spencer and Gillen regularly worked together for several years after their initial encounter, and in 1899 produced a book, The Native Tribes of Central Australia, and their work in central Australia then came to the attention of James Frazer, who maintained an active interest in their ongoing research.

In all, Gillen spent twenty-four years in the interior, during which time, as well as his O. T. L. duties, he was a Sub-Protector of Aborigines and a Special Magistrate. He departed Alice Springs in April, 1899.

Gillen married Amelia Maude Besley on 5 August 1891 in Mount Gambier, South Australia and they had five children. He died, aged fifty-six, from the effects of an obscure, progressive muscle-wasting disease - amyotropic lateral sclerosis - leaving his wife penniless and wondering why her husband had not received the recognition or wealth that Spencer had.